Filtered Genome of Commercial Philippine Varieties of Sugarcane (Saccharum officinarum L.) for the Characterization and Identification of SSRs Associated with Resistance to Philippine Downy Mildew (Peronosclerospora philippinensis)

Authors

• Antonio G. Lalusin, Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Los Baños, Laguna, PhilippinesFollow
• Jhun Lawrence S. Rasco, Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Los Baños, Laguna, Philippines

Publication Date

6-1-2026

Abstract

Sugarcane is a major global source of sugar, with total production reaching 1.89 billion t. Although the Philippines produces about 1.85 million t of sugarcane annually, yields are limited by downy mildew and smut. Developing varieties resistant to these pathogens is the most economical and practical approach to mitigating losses from these biotic stresses. In this study, SSRs related to disease resistance were developed through Next-Generation Sequencing (NGS) of the filtered genomes of sugarcane varieties with known phenotypic responses to downy mildew. Two assemblies based on minimum contig lengths (450 and 900 bp) were performed using SoapDeNovo2. The 900-bp assembly was selected for downstream analyses because it yielded a lower contig count, a higher average contig length, and a larger N50 value. Among the sequenced varieties, VMC 67-611 exhibited the longest assembled filtered genome (16 Mb), while VMC 86-550 displayed the shortest (8 Mb). These differences in observed lengths may be due to varying patterns of hypomethylation across the commercial sugarcane varieties, as previously observed in corn. Contig sequences were also compared against resistance protein databases and were used to mine resistance-associated SSRs. A total of 2,865 resistance-related SSRs were identified, with 50 primers uniquely present in resistant varieties. Notably, susceptible varieties contained almost the same percentage of R-genes as the resistant cultivars. This aligns with the gene-for-gene concept, wherein each resistance gene in a host corresponds to a specific virulence gene in a pathogen; thus, varieties susceptible to downy mildew may maintain resistance to other diseases. Out of 50 designed primer pairs, 25 were used to screen 20 commercial sugarcane varieties, from which 4 primers successfully differentiated resistant and susceptible varieties into distinct clusters. Overall, these developed SSRs may serve as valuable tools for marker-assisted selection in sugarcane.

Recommended Citation

Lalusin, Antonio G. and Rasco, Jhun Lawrence S. (2026) "Filtered Genome of Commercial Philippine Varieties of Sugarcane (Saccharum officinarum L.) for the Characterization and Identification of SSRs Associated with Resistance to Philippine Downy Mildew (Peronosclerospora philippinensis)," The Philippine Agricultural Scientist: Vol. 109: No. 2, Article 16.
Available at: https://www.ukdr.uplb.edu.ph/pas/vol109/iss2/16